Krishna K. Niyogi
Krishna K. Niyogi
Regulation of Photosynthesis
Professor, Associate Chair Plant and Microbial Biology
371A Koshland Hall
Berkeley, California 94720-3102
Phone 510.643.6602
Lab Phone 510.643.6604
Fax 510.642.4995

Ph.D.    Biology    Massachusetts Institute of Technology, 1993
M.Phil.  Biochemistry    University of Cambridge, 1988
B.A.      Biology    The Johns Hopkins University, 1986

Research and Teaching

Understanding and improving photosynthesis

My long-term research goals are to understand how photosynthetic energy conversion works, how it is regulated, and how it might be improved to help meet the world’s needs for food and fuel. We use a wide array of experimental organisms and interdisciplinary approaches to investigate fundamental questions about assembly, regulation, and dynamics of photosynthesis. Current lab members study the biosynthesis and function of photosynthetic pigments, assembly of photosynthetic reaction centers, structure and dynamics of the photosynthetic membrane, mechanisms involved in sensing excess light, and regulation of photosynthetic light harvesting in saturating light. By comparing how photosynthesis works in diverse organisms, we hope to uncover general design principles of natural photosynthesis as well as unique adaptations to different environments.

Algal biology

Eukaryotic algae and cyanobacteria (often collectively referred to simply as “algae”) are relatively simple phototrophic organisms that carry out oxygenic photosynthesis similar to that in land plants. Algae are amazingly diverse in terms of habitat, biochemistry, physiology, and morphology, and they have critical roles in global ecology and biogeochemistry. Aquatic microalgae (phytoplankton) are responsible for approximately half of the net primary production of organic matter on Earth, and they have recently re-emerged as potential next-generation feedstocks for biofuels (http://www.pbs.org/wgbh/nova/tech/algae-fuel.html).

Courses

PMB 120 – Biology of Algae
PMB 120L – Biology of Algae Laboratory
PMB 290 – Plant and Microbial Photosynthesis

Publications

Recent work

Wakao S, Chin BL, Ledford HK, Dent RM, Casero D, Merchant SS, Pellegrini M, Niyogi KK (2014). Phosphoprotein SAK1 is a regulator of acclimation to singlet oxygen in Chlamydomonas reinhardtii. eLife 3: e02286. doi: 10.7554/eLife.02286

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

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

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

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

Kobayashi K, Sasaki D, Noguchi K, Fujinuma D, Komatsu H, Kobayashi M, Sato M, Toyooka K, Sugimoto K, Niyogi KK, Wada H, Masuda T (2013). Photosynthesis of root chloroplasts developed in Arabidopsis lines overexpressing GOLDEN2-LIKE transcription factors. Plant Cell Physiol 54: 1365-1377.

Brooks MD, Sylak-Glassman EJ, Fleming GR, Niyogi KK (2013). A thioredoxin-like/beta-propeller protein maintains the efficiency of light harvesting in Arabidopsis. Proc Natl Acad Sci USA 110: E2733-2740. doi: 10.1073/pnas.1305443110

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

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

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

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

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

Vieler A, Wu G, Tsai C-H, Bullard B, Cornish AJ, Harvey C, Reca I-B, Thornburg C, Achawanantakun R, Buehl CJ, Campbell MS, Cavalier D, Childs KL, Clark TJ, Deshpande R, Erickson E, Ferguson AA, Handee W, Kong Q, Li X, Liu B, Lundback S, Peng C, Roston RL, Sanjaya, Simpson JP, TerBush A, Warakanont J, Zäuner S, Farre EM, Hegg EL, Jiang N, Kuo M-H, Lu Y, Niyogi KK, Ohlrogge J, Osteryoung KW, Shachar-Hill Y, Sears BB, Sun Y, Takahashi H, Yandell M, Shiu S-H, Benning C (2012). Genome, functional gene annotation, and nuclear transformation of the heterokont oleaginous alga Nannochloropsis oceanica CCMP1779. PLoS Genet 8(11): e1003064. doi:10.1371/journal.pgen.1003064

Zaks J, Amarnath K, Kramer DM, Niyogi KK, Fleming GR (2012). A kinetic model of rapidly reversible nonphotochemical quenching. Proc Natl Acad Sci USA 109: 15757-15762.

Tran PT, Sharifi MN, Poddar S, Dent RM, Niyogi KK (2012). Intragenic enhancers and suppressors of phytoene desaturase mutations in Chlamydomonas reinhardtii. PLoS ONE 7(8): e42196. doi:10.1371/journal.pone.0042196

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

Amarnath K, Zaks J, Park SD, Niyogi KK, Fleming GR (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. doi: 10.1073/pnas.1205303109

Fischer BB, Ledford HK, Wakao S, Huang SG, Casero D, Pellegrini M, Merchant SS, Koller A, Eggen RIL, Niyogi KK (2012). SINGLET OXYGEN RESISTANT 1 links reactive electrophile signaling to singlet oxygen acclimation in Chlamydomonas reinhardtii. Proc Natl Acad Sci USA 109: E1302-1311. doi:10.1073/pnas.1116843109

Li Z, Keasling JD, Niyogi KK (2012). Overlapping photoprotective function of vitamin E and carotenoids in ChlamydomonasPlant Physiol 158: 313-323. doi:10.1104/pp.111.181230 (featured in accompanying “On the Inside” article)

Kilian O, Benemann CSE, Niyogi KK, Vick B (2011). High-efficiency homologous recombination in the oil-producing alga, Nannochloropsis sp. Proc Natl Acad Sci USA 108: 21265-21269. doi:10.1073/pnas.1105861108 (featured on the cover and in an accompanying Commentary)

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

Bonente G, Ballottari M, Truong TB, Morosinotto T, Ahn TK, Fleming GR, Niyogi KK, Bassi R (2011). Analysis of LHCSR3, a protein essential for feedback de-excitation in the green alga Chlamydomonas reinhardtii. PLoS Biol 9(1): e1000577. doi:10.1371/journal.pbio.1000577

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

 

Highlights of older work

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 462: 518-52.

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.

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

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, 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.

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.

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

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.

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.

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.

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.

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.

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

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.

Havaux M, Niyogi KK (1999).  The violaxanthin cycle protects plants from photo-oxidative damage by more than one mechanism.  Proc Natl Acad Sci USA 96:  8762–8767.

Honors and Awards

HHMI-GBMF Investigator - Howard Hughes Medical Institute and the Gordon and Betty Moore Foundation - 2011
Charles Albert Schull Award - American Society of Plant Biologists - 2005
Melvin Calvin Award - International Society of Photosynthesis Research - 2001
Presidential Early Career Award for Scientists and Engineers - USDA - 1998
Searle Scholar - Searle Scholars Program/The Chicago Community Trust - 1998