KNiyogi

Krishna K. Niyogi
Krishna K.
Niyogi
Email: 
niyogi@berkeley.edu
Lab Phone: 
510-643-6604

 

Education
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
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, in press. 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 Chlamydomonas. Plant 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.

Jung H-S, Niyogi KK (2010). Mutations in Arabidopsis YCF20-like genes affect thermal dissipation of excess absorbed light energy. Planta 231:  923-937.

Meinecke L, Alawady A, Schroda M, Willows R, Kobayashi MC, Niyogi KK, Grimm B, Beck CF (2010). Chlorophyll-deficient mutants of Chlamydomonas reinhardtii that accumulate magnesium protoporphyrin IX. Plant Mol Biol 72:  643-658.

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

Jung H-S, Okegawa Y, Shih, PM, Kellog E, Abdel-Ghany SE, Pilon M, Sjölander K, Shikanai T, Niyogi KK (2010). Arabidopsis thaliana PGR7 encodes a conserved chloroplast protein that is necessary for efficient photosynthetic electron transport. PLoS ONE 5(7): e11688. doi:10.1371/journal.pone.0011688.

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

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

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

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.

Cohu CM, Abdel-Ghany SE, Gogolin-Reynolds KA, Onofrio AM, Bodecker JR, Kimbrel JA, Niyogi KK, Pilon M (2009). Copper delivery by the copper chaperone for chloroplast and cytosolic copper/zinc-superoxide dismutases: regulation and unexpected phenotypes in an Arabidopsis mutant. Mol Plant 2: 1336-1350.

Sirikhachornkit A, Shin JW, Baroli I, Niyogi KK (2009). Replacement of alpha-tocopherol by beta-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.

Highlights of Older Work
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